This web page was produced as an assignment for Genetics 564, an undergraduate course at UW-Madison.
What is a homolog?
In genetics, homology is used to identify how similar a DNA sequence is across various organisms--indicating the linkage to a common ancestor [1]. Together, this information can be utilized to identify potential model organisms for later studies, as the percent of how identical the two DNA sequences are can be identified. This percent can then indicate which organisms will provide the greatest opportunity cost to study with, while also presenting some organisms with homolog genes that have not yet been studied.
To identify possible homologs, an initial search on HomoloGene can prove to be quite useful. Homologene contains a large database of homology groups from various gene sequence data sets that can then be used for model organism comparison. Should HomoloGene fail to provide enough information, BLAST can also be utilized to compare the homo sapien, or human, mRNA sequence to the chosen FASTA sequence. While this allows for a direct comparison, it also allows for further protein phylogeny to be identified as well. For more information on PSEN1 phylogeny, click here.
To identify possible homologs, an initial search on HomoloGene can prove to be quite useful. Homologene contains a large database of homology groups from various gene sequence data sets that can then be used for model organism comparison. Should HomoloGene fail to provide enough information, BLAST can also be utilized to compare the homo sapien, or human, mRNA sequence to the chosen FASTA sequence. While this allows for a direct comparison, it also allows for further protein phylogeny to be identified as well. For more information on PSEN1 phylogeny, click here.
Model organisms
Using both HomoloGene and BLAST, a list of model organisms for studying the influence of presenilin 1 on Alzheimer's can be established. While the top portion of the list contains organisms with relatively high similarity to that of human PSEN1 and are the ideal model organism candidates, additional organisms with presenilin 1 homologs, such as Arabidopsis thaliana, Caenorhabditis elegans, and zebrafish were included to illustrate just how vast gene homology stretches.
This list was then consorted when choosing model organisms for the Alzheimer's research, namely Mus musculus (mouse), with a relatively identical sequence, and Danio rerio (zebrafish), which can be used to study neurological function to a different extent than that of mice.
This list was then consorted when choosing model organisms for the Alzheimer's research, namely Mus musculus (mouse), with a relatively identical sequence, and Danio rerio (zebrafish), which can be used to study neurological function to a different extent than that of mice.
Bonobo (Pan paniscus)
Gene Name: Pan paniscus PSEN1 Accession Number: XM_003824135.2 FASTA 99% Identical E Value: 0.0 Chimpanzee (Pan troglodytes) Gene Name: Pan troglodytes PSEN1 Accession Number: XM_001150037.4 FASTA 99% Identical E Value: 0.0 Guinea Pig (Cavia porcellus) Gene Name: Cavia porcellus PSEN1 Accession Number: XM_003472398.2 FASTA 86% Identical E Value: 0.0 Arabidopsis thaliana Gene Name: Presenilin-1 Accession Number: NC_003070 FASTA 27% Identical E Value: 0.0 |
Cat (Felis catus)
Gene Name: Felis catus PSEN1 Accession Number: XM_003987805.2 FASTA 87% Identical E Value: 0.0 Dog (Canis lupus familiaris) Gene Name: Canis lupus familiaris PSEN1 Accession Number: NM_001002943.2 FASTA 86% Identical E Value: 0.0 Mouse (Mus musculus) Gene Name: Mus musculus PSEN1 Accession Number: NM_008943.2 FASTA 85% Identical E Value: 0.0 Caenorhabditis elegans Gene Name: Sel-12 Accession Number: AF171064 FASTA 49% Identical E Value: 0.0 |
Chicken (Gallus gallus)
Gene Name: Gallus gallus PSEN1 Accession Number: NM_204163.1 FASTA 80% Identical E Value: 0.0 Gorilla (Gorilla gorilla) Gene Name: Gorilla gorilla gorilla PSEN1 Accession Number: XM_004055415.1 FASTA 99% Identical E Value: 0.0 Rat (Rattus norvegicus) Gene Name: Rattus norvegicus PSEN1 Accession Number: NM_019163.3 FASTA 88% Identical E Value: 0.0 Zebrafish (Danio rerio) Gene Name: Presenilin 1 Accession Number: NC_007128 FASTA 72% Identical E Value: 0.0 |
Discussion
While all the homologs identified have relatively identical sequences to that of human PSEN1, this is understandable. Namely, as presenilin 1 is involved in neural cell regulation, it would be important for every mammal to have. As the necessity for neurological regulation is unnecessary in both Arabidopsis and C. elegans, it is no surprise to witness a less identical gene sequence to that of humans. While these would not be useful model organisms, both indicate just how far a gene can be traced.
In addition, this gene homology can then be used to find protein homology, as gene homology provides a reasonable starting place for more research. For protein homology information, click here.
Mentioned earlier, mice and zebrafish, both with relatively identical PSEN1 sequences to that of humans were chosen to use for research and the proposed specific aims. To read more on the proposed aims, click here.
In addition, this gene homology can then be used to find protein homology, as gene homology provides a reasonable starting place for more research. For protein homology information, click here.
Mentioned earlier, mice and zebrafish, both with relatively identical PSEN1 sequences to that of humans were chosen to use for research and the proposed specific aims. To read more on the proposed aims, click here.
REFERENCES